ArticleNature methods2014
Measuring similarity between dynamic ensembles of biomolecules.
Article in Nature methods, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Assessing the contribution of rare DNA states to cancer mutational signatures using sequence-specific conformational fingerprinting.Nature communications · 2026Article
- Assessing the contribution of rare DNA states to cancer mutational signatures using sequence-specific conformational fingerprinting.Research square · 2025Article
- Determining accurate conformational ensembles of intrinsically disordered proteins at atomic resolution.Nature communications · 2025Article
- NMR structures and magnetic force spectroscopy studies of small molecules binding to models of an RNA CAG repeat expansion.bioRxiv : the preprint server for biology · 2024Article
- Article
- Distance-Based Metrics for Comparing Conformational Ensembles of Intrinsically Disordered Proteins.Biophysical journal · 2020Article
- Salt Dependence of A-Form RNA Duplexes: Structures and Implications.The journal of physical chemistry. B · 2019Article
- NMR characterization of RNA small molecule interactions.Methods (San Diego, Calif.) · 2019Review
- Conformations of an RNA Helix-Junction-Helix Construct Revealed by SAXS Refinement of MD Simulations.Biophysical journal · 2019Article
- Increasing the length of poly-pyrimidine bulges broadens RNA conformational ensembles with minimal impact on stacking energetics.RNA (New York, N.Y.) · 2018Article
- Acceleration of biomolecular kinetics in Gaussian accelerated molecular dynamics.The Journal of chemical physics · 2018Article
- Conformational ensemble comparison for small molecules in drug discovery.Journal of computer-aided molecular design · 2018Article
- High-performance virtual screening by targeting a high-resolution RNA dynamic ensemble.Nature structural & molecular biology · 2018Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- Statistical Measures to Quantify Similarity between Molecular Dynamics Simulation Trajectories.Entropy (Basel, Switzerland) · 2017Article
- Insights into Watson-Crick/Hoogsteen breathing dynamics and damage repair from the solution structure and dynamic ensemble of DNA duplexes containing m1A.Nucleic acids research · 2017Article
- Determination of the conformational ensemble of the TAR RNA by X-ray scattering interferometry.Nucleic acids research · 2017Article
- Modulating RNA Alignment Using Directional Dynamic Kinks: Application in Determining an Atomic-Resolution Ensemble for a Hairpin using NMR Residual Dipolar Couplings.Journal of the American Chemical Society · 2015Article
- ENCORE: Software for Quantitative Ensemble Comparison.PLoS computational biology · 2015Article
- Unveiling Inherent Degeneracies in Determining Population-Weighted Ensembles of Interdomain Orientational Distributions Using NMR Residual Dipolar Couplings: Application to RNA Helix Junction Helix Motifs.The journal of physical chemistry. B · 2015Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
We present a simple and general approach termed REsemble for quantifying population overlap and structural similarity between ensembles. This approach captures improvements in the quality of ensembles determined using increasing input experimental data--improvements that go undetected when conventional methods for comparing ensembles are used--and reveals unexpected similarities between RNA ensembles determined using NMR and molecular dynamics simulations.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.